14 variations found. LOC_Os12g04360 (calmodulin-like protein 1; putative; expressed), ranging from 1,851,397 bp to 1,852,196 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Color | Explain | Details |
|---|---|---|
| red | High impact variants defined by snpEff | 'STOP_LOST', 'START_LOST', 'STOP_GAINED', 'FRAME_SHIFT' et. al., the details can be found at http://snpef f.sourceforge.net/SnpEff_manual.html#eff. |
| purple | 'Damaging' or 'probably damaging' non-synonymous SNPs defined by PolyPhen-2 | This is a qualitative result of nonsynonymous SNP annotation, where 'damaging' or 'probably damaging' means that the variant is more likely to affect protein function. Details can be found here. |
| Var ID | Chrom | Position | Primary Allele | Secondary Allele | Primary Allele Frequency | DEL Frequency | Var | GWAS Results | Effect |
|---|---|---|---|---|---|---|---|---|---|
| vg1201851427 (J) | chr12 | 1851427 | T | G | 55.00% | 0.55% | G -> T |
mr1026 (All); LR P-value: 6.56E-36;
mr1063 (All); LR P-value: 1.49E-52; mr1076 (All); LR P-value: 2.15E-26; mr1083 (All); LR P-value: 3.83E-23; mr1085 (All); LR P-value: 2.10E-29; mr1088 (All); LR P-value: 1.12E-63; mr1104 (All); LR P-value: 1.25E-33; mr1108 (All); LR P-value: 6.02E-47; mr1111 (All); LR P-value: 8.31E-47; mr1112 (All); LR P-value: 1.57E-45; mr1131 (All); LR P-value: 7.83E-20; mr1139 (All); LR P-value: 1.93E-40; mr1144 (All); LR P-value: 1.70E-42; mr1145 (All); LR P-value: 7.85E-28; mr1151 (All); LR P-value: 3.34E-09; mr1161 (All); LR P-value: 1.04E-35; mr1204 (All); LR P-value: 8.01E-31; mr1221 (All); LR P-value: 3.91E-29; mr1224 (All); LR P-value: 6.75E-35; mr1225 (All); LR P-value: 9.70E-34; mr1226 (All); LR P-value: 4.04E-29; mr1233 (All); LR P-value: 1.33E-11; mr1234 (All); LR P-value: 4.40E-46; mr1237 (All); LR P-value: 1.57E-30; mr1246 (All); LR P-value: 4.61E-66; mr1260 (All); LR P-value: 3.53E-09; mr1261 (All); LR P-value: 6.00E-16; mr1264 (All); LR P-value: 2.25E-24; mr1342 (All); LR P-value: 6.73E-09; mr1404 (All); LR P-value: 4.23E-34; mr1411 (All); LR P-value: 5.22E-25; mr1436 (All); LR P-value: 1.62E-28; mr1437 (All); LR P-value: 5.78E-41; mr1560 (All); LR P-value: 2.86E-31; mr1620 (All); LR P-value: 3.51E-39; mr1878 (All); LR P-value: 2.55E-34; mr1973 (All); LR P-value: 2.09E-80; mr1063_2 (All); LR P-value: 1.55E-51; mr1065_2 (All); LR P-value: 9.34E-64; mr1070_2 (All); LR P-value: 9.34E-46; mr1083_2 (All); LR P-value: 2.22E-32; mr1088_2 (All); LR P-value: 4.85E-80; mr1091_2 (All); LR P-value: 5.71E-49; mr1094_2 (All); LR P-value: 7.95E-47; mr1096_2 (All); LR P-value: 3.32E-61; mr1108_2 (All); LR P-value: 3.28E-56; mr1110_2 (All); LR P-value: 1.35E-37; mr1111_2 (All); LR P-value: 2.96E-51; mr1112_2 (All); LR P-value: 5.19E-64; mr1121_2 (All); LR P-value: 1.02E-53; mr1131_2 (All); LR P-value: 1.21E-18; mr1144_2 (All); LR P-value: 5.77E-52; mr1147_2 (All); LR P-value: 9.47E-13; mr1161_2 (All); LR P-value: 5.57E-35; mr1189_2 (All); LR P-value: 5.10E-12; mr1199_2 (All); LR P-value: 1.64E-17; mr1208_2 (All); LR P-value: 3.12E-38; mr1224_2 (All); LR P-value: 4.44E-39; mr1226_2 (All); LR P-value: 1.89E-40; mr1234_2 (All); LR P-value: 3.04E-58; mr1246_2 (All); LR P-value: 1.10E-80; mr1264_2 (All); LR P-value: 5.22E-39; mr1270_2 (All); LR P-value: 1.93E-28; mr1316_2 (All); LR P-value: 2.61E-22; mr1325_2 (All); LR P-value: 2.86E-12; mr1404_2 (All); LR P-value: 4.34E-51; mr1514_2 (All); LR P-value: 3.75E-13; mr1734_2 (All); LR P-value: 1.27E-10; mr1744_2 (All); LR P-value: 1.62E-16; mr1745_2 (All); LR P-value: 1.34E-40; mr1782_2 (All); LR P-value: 3.03E-10; mr1878_2 (All); LR P-value: 8.43E-37; mr1932_2 (All); LR P-value: 5.01E-31; mr1970_2 (All); LR P-value: 1.29E-61; mr1973_2 (All); LR P-value: 7.77E-101 |
LOC_Os12g04360.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g04360.1 Alt: T| start_lost HIGH(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 93.928; most accessible tissue: Zhenshan97 root, score: 98.522 |
| vg1201851468 (J) | chr12 | 1851468 | C | Unkown | 99.80% | 0.08% | C -> CGT | NA |
The average chromatin accessibility score: 93.190; most accessible tissue: Zhenshan97 root, score: 98.237
|
| vg1201851550 (J) | chr12 | 1851550 | C | Unkown | 99.50% | 0.11% | C -> T | NA |
LOC_Os12g04360.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os12g04370.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 91.639; most accessible tissue: Zhenshan97 root, score: 97.540 |
| vg1201851688 (J) | chr12 | 1851688 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os12g04360.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os12g04370.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 81.783; most accessible tissue: Zhenshan97 root, score: 94.761 |
| vg1201851781 (J) | chr12 | 1851781 | C | T | 99.60% | 0.00% | C -> T | NA |
LOC_Os12g04360.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os12g04370.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 80.531; most accessible tissue: Zhenshan97 panicle, score: 94.026 |
| vg1201851796 (J) | chr12 | 1851796 | G | T | 99.80% | 0.00% | G -> T | NA |
LOC_Os12g04360.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os12g04370.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 80.482; most accessible tissue: Zhenshan97 panicle, score: 94.112 |
| vg1201851799 (J) | chr12 | 1851799 | C | A | 99.80% | 0.00% | C -> A | NA |
LOC_Os12g04360.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os12g04370.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 80.867; most accessible tissue: Zhenshan97 panicle, score: 94.112 |
| vg1201851886 (J) | chr12 | 1851886 | C | G | 58.60% | 25.45% | C -> G | NA |
LOC_Os12g04360.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g04360.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 77.267; most accessible tissue: Zhenshan97 panicle, score: 93.020 |
| vg1201852107 (J) | chr12 | 1852107 | C | CT | 99.20% | 0.00% | C -> CT | NA |
LOC_Os12g04360.1 Alt: CT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g04370.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.789; most accessible tissue: Minghui63 panicle, score: 89.444 |
| vg1201852108 (J) | chr12 | 1852108 | TG | T | 64.10% | 0.59% | T -> TG | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g04360.1 Alt: TG| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g04370.1 Alt: TG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.798; most accessible tissue: Minghui63 panicle, score: 89.444 |
| vg1201852122 (J) | chr12 | 1852122 | T | C | 99.10% | 0.00% | T -> C | NA |
LOC_Os12g04360.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g04370.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.150; most accessible tissue: Minghui63 panicle, score: 89.949 |
| vg1201852141 (J) | chr12 | 1852141 | A | AC | 55.20% | 0.57% | AC -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g04360.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g04370.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.093; most accessible tissue: Minghui63 panicle, score: 90.184 |
| vg1201852180 (J) | chr12 | 1852180 | GT | G | 55.00% | 0.02% | G -> GT | NA |
LOC_Os12g04360.1 Alt: GT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g04370.1 Alt: GT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 76.182; most accessible tissue: Minghui63 panicle, score: 89.702 |
| STR1201852181 (J) | chr12 | 1852181 | TTGTTTG TTTGT | TTGTTTG TTTG | 62.00% | 0.00% | TTGTTTGTTT G -> TTGTTTGTTT GT | NA |
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